Bacillus bacteria for use in treating and preventing infection in aquatic animals

ABSTRACT

Disclosed herein are microbiocidal compositions that include spore-forming strains of  Bacillus . The compositions may be utilized to treat or prevent disease in aquatic animals such as farmed fish or crustaceans.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of priority under 35 U.S.C. §119(e) to U.S. Provisional Applications No. 61/480,622, filed on Apr. 29, 2011, the content of which is incorporated herein by reference in its entirety.

BACKGROUND

The field of the present invention relates to compositions and methods for treating or preventing disease in aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp). In particular, the present invention relates to compositions and methods comprising or utilizing spore forming strains of Bacillus for treating or preventing diseases such as enteric septicemia in aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp).

Recently, attention has focused on the use of probiotics to improve animal health and nutrition. The interest in probiotic bacteria for aquaculture application follows their use in human medicine and agriculture (Fuller and Turvey 1971; Roach and Tannock 1980; Fuller 1987; Smoragiewicz et al. 1993; Fuller 1997), in which microorganisms are generally administered as live supplements in feed (Fuller 1997). The beneficial effect to the host has been reported to be nutritional, immunological, and/or to involve competitive exclusion whereby potential pathogens are outcompeted in the digestive tract (Smoragiewicz et al. 1993). Probiotics have been shown to be effective in controlling various infectious diseases in aquaculture, including furunculosis caused by A, salmonicida in rainbow trout (Irianto and Austin 2002), saprolegniosis by Saprolegnia parasitica in the short-finned eel Anguilla australis (Lategan et al. 2004), edwardsiellosis by Edwardsiella tarda in the European eel Anguilla anguilla (Chang and Liu 2002), lactococcosis and streptococcosis by Lactococcus garvieae and Streptococcus iniae, respectively, in rainbow trout (Brunt and Austin 2005), and disease caused by Vibrio anguillarum in Atlantic cod fry (Gildberg and Mikkelsen 1998). The bacteria used for probiotics include Enterococcus spp., Aeromonas spp., Vibrio spp., and lactic acid bacteria (Gildberg and Mikkelsen 1998; Chang and Liu 2002; Irianto and Austin 2002; Lategan et al. 2004; Brunt and Austin 2005). Most of the probiotic bacteria were isolated from the intestine of aquaculture animals (Gildberg and Mikkelsen 1998; Irianto and Austin 2002; Lategan et al. 2004; Brunt and Austin 2005). Some bacteria isolated from the habitats of aquaculture animals also showed probiotic activity (Rengpipat et al. 1998). The antimicrobial activity against a particular pathogen is used as a primary criterion for selection of potential probiotic bacteria (Rengpipat et al. 1998; Irianto and Austin 2002). The collection of bacterial strains used in this study was derived from previous studies of soil-derived bacteria useful for biological control of diseases in plants and for their plant growth-promoting abilities (Kloepper et al. 2004), as well as bacterial cultures derived from catfish intestinal samples identified in this study.

SUMMARY

Disclosed are microbiocidal compositions that kill or inhibit the growth of bacteria. The composition may kill or inhibit the growth of pathogenic bacteria such as bacteria associated with enteric septicemia. The compositions comprise an effective amount of a spore-forming strain of Bacillus for killing or inhibiting the growth of bacteria, such as bacteria associated with enteric septicemia. In some embodiments, the disclosed compositions are formulated as feed compositions for aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp). In other embodiments, the disclosed compositions may be formulated for administering to an environment where aquatic animals live or are raised.

Preferably, the compositions comprise a spore-forming strain of the genus Bacillus at a concentration of at least about 10⁴ CFU/g of feed or per ml of water. More preferably, the spore-forming strain of the genus Bacillus is present in the composition at a concentration of at least about 10⁵ CFU/g of feed or per ml of water. Even more preferably, the spore-forming strain of the genus Bacillus is present in the composition at a concentration of at least about 10⁶ CFU/g of feed or per ml of water or at least about 10⁷ CFU/g of feed or per ml of water. A suitable concentration range may include 10⁴-10⁷ CFU/g of feed or per ml of water or sub-ranges there within.

The compositions may comprise a single strain of the genus Bacillus. Alternatively, the compositions may comprise a mixture of strains of the genus Bacillus.

The compositions typically comprise an effective amount the spore-forming strain of the genus Bacillus to kill or inhibit the growth of one or more pathogenic microorganism. For example, pathogenic bacteria may be selected from a group consisting of Aeromonas hydrophila, Edwardsiella ictaluri, Edwardsiella tarda, Flavobacterium columnare, Streptococcus iniae, and Yersinia ruckeri. Pathogenic fungi may include the oomycete fungus Saprolegnia.

The disclosed compositions comprise a spore-forming strain of Bacillus. The compositions may comprise further agents for killing or preventing the growth of pathogenic microorganisms. In some embodiments, the compositions further comprise a bacteriophage that infects E. ictaluri (e.g., φeiAU). The disclosed compositions may comprise antibiotic agents such as sulfadimethoxine, ormetoprim, and/or florfenical. The disclosed compositions further may comprise an attenuated microbe as a vaccine agent (e.g., an attenuated strain of E. ictaluri).

Also disclosed are methods for treating or preventing disease in an animal comprising administering the presently disclosed compositions. For example, the methods may include administering a feed composition comprising a spore-forming strain of Bacillus to aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp). The methods further may include administering a microbiocidal composition as disclosed herein to an environment where aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) live and/or are raised. The methods may be utilized to treat or prevent diseases such as enteric septicemia. The method may be utilized to treat or prevent infection in aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) by pathogenic microorganisms such as Aeromonas hydrophila, Edwardsiella ictaluri, Edwardsiella tarda, Flavobacterium columnare, Streptococcus iniae, Yersinia ruckeri, Vibrio species and/or the oomycete fungus Saprolegnia.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a photomicrograph at 10× magnification of a soft agar overlay demonstrating growth inhibition of A. hydrophila strain ML09-119 (on the right) by Bacillus strain AP102 (on the left).

FIG. 2. illustrates Bacillus strain CFUs/g of catfish intestine, after feeding with Bacillus-amended or non-amended feed (n=3 animals per Bacillus strain).

FIG. 3 illustrates cumulative daily mortality of channel catfish fingerlings exposed to ESC with and without being feed Bacillus-amended feed.

FIG. 4. illustrates the concentration of Bacillus strain CFUs/g in catfish intestine, after feeding with Bacillus-amended or non-amended feed (n=3 animals per Bacillus strain).

FIG. 5. Illustrates the daily mean cumulative mortality of (A) channel catfish in static system with 20-30 min daily water exchange and (B) channel catfish with 5-7 h flow through water daily, or (C) striped catfish in static system with 20-30 min daily water exchange, fed with and without addition of Bacillus strains and challenged with E. ictaluri. All values are means of four replicates per treatment. Treatments: (◯) Control, (●) AP79, (▾) AP193L, (Δ) AB01, (▪) AP143, and (♦) AP254L.

DETAILED DESCRIPTION

Disclosed herein are microbiocidal compositions. The disclosed microbiocidal compositions may be described using several definitions as discussed below.

Unless otherwise specified or indicated by context, the terms “a”, “an”, and “the” mean “one or more.” In addition, singular nouns such as “a strain of Bacillus” should be interpreted to mean “one or more strains of Bacillus,” unless otherwise specified or indicated by context.

As used herein, “about”, “approximately,” “substantially,” and “significantly” will be understood by persons of ordinary skill in the art and will vary to some extent on the context in which they are used. If there are uses of the term which are not clear to persons of ordinary skill in the art given the context in which it is used, “about” and “approximately” will mean plus or minus≦10% of the particular term and “substantially” and “significantly” will mean plus or minus>10% of the particular term.

As used herein, the terms “include” and “including” have the same meaning as the terms “comprise” and “comprising.”

The presently disclosed composition and methods include or utilize a spore-forming strain of the Bacillus genus. The genus Bacillus as used herein refers to a genus of Gram-positive, rod-shaped bacteria which are members of the division Firmicutes. Under stressful environmental conditions, the Bacillus bacteria produce oval endospores that can stay dormant for extended periods. Bacillus bacteria may be characterized and identified based on the nucleotide sequence of their 16S rRNA or a fragment thereof (e.g., approximately a 1000 nt, 1100 nt, 1200 nt, 1300 nt, 1400 nt, or 1500 nt fragment of 16S rRNA or rDNA nucleotide sequence). Bacillus bacteria may include, but are not limited to B. acidiceler, B. acidicola, B. acidiproducens, B. aeolius, B. aerius, B. aerophilus, B. agaradhaerens, B. aidingensis, B. akibai, B. alcalophilus, B. algicola, B. alkalinilrilicus, B. alkalisediminis, B. alkalitelluris, B. altitudinis, B. alveayuensis, B. amyloliquefaciens, B. anthracis, B. aquimaris, B. arsenicus, B. aiyabhattai, B. asahii, B. atrophaeus, B. aurantiacus, B. azotoformans, B. badius, B. barbaricus, B. bataviensis, B. beijingensis, B. benzoevorans, B. beveridgei, B. bogoriensis, B. boroniphilus, B. butanolivorans, B. canaveralius, B. carboniphilus, B. cecembensis, B. cellulosilylicus, B. cereus, B. chagannorensis, B. chungangensis, B. cibi, B. circulars, B. clarkii, B. clausii, B. coagulans, B. coahuilensis, B. cohnii, B. decisifrondis, B. decolorationis, B. drentensis, B. farraginis, B. fastidiosus, B. firmus, B. flexus, B. foraminis, B. fordii, B. fortis, B. fumarioli, B. funiculus, B. galactosidilyticus, B. galliciensis, B. gelatini, B. gibsonii, B. ginsengi, B. ginsengihumi, B. graminis, B. halmapalus, B. halochares, B. halodurans, B. hemicellulosilyticus, B. herberisteinensis, B. horikoshi, B. horneckiae, B. horti, B. humi, B. hwajinpoensis, B. idriensis, B. indicus, B. infantis, B. infernus, B. isabeliae, B. isronensis, B. jeotgali, B. koreensis, B. korlensis, B. kribbensis, B. krulwichiae, B. lehensis, B. lentus, B. licheniformis, B. litoralis, B. locisalis, B. luciferensis, B. luteolus, B. macauensis, B. macyae, B. mannanilyticus, B. marisflavi, B. marmarensis, B. massiliensis, B. megaterium, B. methanolicus, B. methylotrophicus, B. mojavensis, B. muralis, B. murimartini, B. mycoides, B. nanhaiensis, B. nanhaiisediminis, B. nealsonii, B. neizhouensis, B. niabensis, B. niacini, B. novalis, B. oceanisediminis, B. odysseyi, B. okhensis, B. okuhidensis, B. oleronius, B. oshimensis, B. panaciterrae, B. patagoniensis, B. persepolensis, B. plakortidis, B. pocheonensis, B. polygoni, B. pseudoalcaliphilus, B. pseudofirmus, B. pseudomycoides, B. psychrosaccharolyticus, B. pumilus, B. qingdaonensis, B. rigui, B. ruris, B. safensis, B. salarius, B. saliphilus, B. schlegelii, B. selenatarsenatis, B. selenitireducens, B. seohaeanensis, B. shackletonii, B. siamensis, B. simplex, B. siralis, B. smithii, B. soli, B. solisalsi, B. sonorensis, B. sporothermodurans, B. stratosphericus, B. subterraneus, B. subtilis, B. taeansis, B. tequilensis, B. thermantarcticus, B. thermoamylovorans, B. thermocloacae, B. thermolactis, B. thioparans, B. thuringiensis, B. tripoxylicola, B. tusciae, B. vallismortis, B. vedderi, B. vietnamensis, B. vireti, B. wakoensis, B. weihenstephanensis, B. xiaoxiensis, and mixtures or blends thereof.

The disclosed compositions and methods may include or utilize B. subtilis or a Bacillus species that is closely related to B. subtilis. The partial sequence of B. subtilis strain NH.259 16S ribosomal rDNA (GenBank Accession No. EU627171.1) is provided herein as SEQ ID NO:1. A Bacillus species that is closely related to B. subtilis may be defined as a species comprising a 16S rDNA sequence comprising SEQ ID NO:1 or comprising a 16S rDNA sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:1.

The disclosed compositions and methods may include or utilize B. amyloliquefaciens or a Bacillus species that is closely related to B. amyloliquefaciens. The partial sequence of B. amyloliquefaciens strain Chilli-1 16S ribosomal rDNA (GenBank Accession No. HQ021420.1) is provided herein as SEQ ID NO:2. A Bacillus species that is closely related to B. amyloliquefaciens may be defined as a species comprising a 16S rDNA sequence comprising SEQ ID NO:2 or comprising a 16S rDNA sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:2.

The disclosed compositions and methods may include or utilize a Bacillus species that has a 16S rDNA closely related to a selected consensus sequence for Bacillus spp. strains. A consensus sequence for Bacillus spp. strains is provided as SEQ ID NO:3. The disclosed compositions and methods may include or utilize a Bacillus species that comprises a 16S rDNA sequence comprising SEQ ID NO:3 or comprising a 16S rDNA sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3.

“Percentage sequence identity” may be determined by aligning two sequences of equivalent length using the Basic Local Alignment Search Tool (BLAST) available at the National Center for Biotechnology Information (NCBI) website (i.e., “bl2seq” as described in Tatiana A. Tatusova, Thomas L. Madden (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett. 174:247-250, incorporated herein by reference in its entirety). For example, percentage sequence identity between SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3 may be determined by aligning these two sequences using the online BLAST software provided at the NCBI website.

“Percentage sequence identity” between two deoxyribonucleotide sequences may also be determined using the Kimura 2-parameter distance model which corrects for multiple hits, taking into account transitional and transversional substitution rates, while assuming that the four nucleotide frequencies are the same and that rates of substitution do not vary among sites (Nei and Kumar, 2000) as implemented in the MEGA 4 (Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599), preferably version 4.0.2 or later. The gap opening and extension penalties are set to 15 and 6.66 respectively. Terminal gaps are not penalized. The delay divergent sequences switch is set to 30. The transition weight score is 35 set to 0.5, as a balance between a complete mismatch and a matched pair score. The DNA weight matrix used is the IUB scoring matrix where x's and n's are matches to any IUB ambiguity symbol, and all matches score 1.9, and all mismatched score O.

Suitable strains of Bacillus for the disclosed compositions and methods include strains disclosed in the Examples provided herein. These suitable strains include, but are not limited to Bacillus subtilis strain AB01, and Bacillus amyloliquefaciens strains AP79, AP143, AP193L, and AP254L, deposited at the United Stated Department of Agriculture on Apr. 27, 2012, under accession numbers NRRL B-50745, NRRL B-50741, NRRL B-50742, and NRRL B-50743, and NRRL B-50744, respectively.

The presently disclosed strains of Bacillus exhibit antibiotic activity in various bacterial pathogens of aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) including species of Edwardsiella bacteria such as Edwardsiella ictaluri. In some embodiments, the disclosed bacteriophage or variants thereof may be utilized in methods for killing or preventing the growth of pathogenic bacteria or fungi of aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp). In particular, the methods may be utilized to control or prevent the infection or colonization of catfish (e.g., Ictaluri punctatus Rafinesque) by pathogenic bacteria or fungi or colonization of environments in which catfish live or are raised (e.g., aquaculture ponds). The disclosed methods also may be utilized to detect the presence of bacteria in a sample (e.g., a sample obtained from infected aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp), or a sample isolated from an environment in which aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) live or are raised).

Also disclosed are methods of using the disclosed strains of Bacillus for removing pathogenic bacteria or fungi from environments or instruments used to raise aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp), thereby reducing the likelihood that the bacteria or fungi may be passed to the aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp).

Also disclosed are methods of using the presently disclosed strains of Bacillus to treat or prevent diseases caused by pathogenic bacteria or fungi (e.g., treating or preventing enteric septicemia of catfish (ESC)). In further embodiments, in order to control or inhibit the growth of pathogenic bacteria or fungi or to remove pathogenic bacteria or fungi, the presently disclosed strains of Bacillus may be administered to an environment (e.g., a pond) or instrument, or the presently disclosed strains of Bacillus may be administered to aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp).

The term “catfish” refers to a fish belonging to the genus Ictaluri. Catfish may include the species Ictaluri punctatus Rafinesque.

The presently disclosed strains of spore-forming Bacillus may be utilized to kill or prevent the growth of bacteria or fungi that are pathogenic to aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp). “Pathogenic bacteria” may include, but are not limited to, A. hydrophila, E. ictaluri, E. tarda, F. columnare, Streptococcus iniae, F. columnare, Yersinia ruckeri, and Vibrio species. “Pathogenic fungi may include, but are not limited to the oomycete fungus Saprolegnia.

The disclosed strains of spore-forming Bacillus may be administered with additional agents for killing or preventing the growth of pathogenic bacteria or fungi. Additional agents may include antibiotics such as sulfadimethoxine and ormetoprim, attenuated strains of bacteria (e.g., an attenuated strain of E. ictaluri), florfenical, and bacteriophage. Bacteriophage may include the bacteriophage designated as ΦeiAU, deposited with the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Va., 20110-2209, USA, on Sep. 15, 2009 under accession no. PTA-10342.

The term “sample” is used herein in its broadest sense. A sample may comprise a biological sample from an animal (e.g., a biological sample obtained from aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp)) or a sample taken from an environment (e.g., a water sample from a pond or a swabbed surface sample taken from a container or instrument).

ILLUSTRATIVE EMBODIMENTS

The following embodiments are illustrative and are not intended to limit the claimed subject matter.

Embodiment 1. A feed composition comprising one or more spore-forming strains of the genus Bacillus.

Embodiment 2. The composition of embodiment 1, wherein the spore-forming strain of the genus Bacillus is Bacillus subtilis or a Bacillus species comprising a 16S rDNA sequence comprising SEQ ID NO:1 or comprising a 16S rDNA sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 1.

Embodiment 3. The composition of embodiment 1, wherein the spore-forming strain of the genus Bacillus is Bacillus amyloliquefaciens or a Bacillus species comprising a 16S rDNA sequence comprising SEQ ID NO:2 or comprising a 16S rDNA sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:2.

Embodiment 4. The composition of embodiment 1, wherein the spore-forming strain of the genus Bacillus is a Bacillus species comprising a 16S rDNA sequence comprising SEQ ID NO:3 or comprising a 16S rDNA sequence having at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:3.

Embodiment 5. The composition of embodiment 1, wherein the spore-forming strain of the genus Bacillus is a strain selected from a group consisting of AB01, AP79, AP143, AP193L, AP254L, deposited at the United Stated Department of Agriculture on Apr. 27, 2012, under accession numbers NRRL B-50745, NRRL B-50741, NRRL B-50742, NRRL B-50743, and NRRL B-50744, respectively.

Embodiment 6. The composition of any of the foregoing embodiments, wherein the feed composition is a feed composition for aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp).

Embodiment 7. The composition of any of the foregoing embodiments, wherein the spore-forming strain of the genus Bacillus is present in the composition at a concentration of at least about 10⁴ CFU/g of feed.

Embodiment 8. The composition of any of the foregoing embodiments, wherein the spore-forming strain of the genus Bacillus is present in the composition at a concentration of at least about 10⁵ CFU/g of feed.

Embodiment 8. The composition of any of the foregoing embodiments, wherein the spore-forming strain of the genus Bacillus is present in the composition at a concentration of at least about 10⁶ CFU/g of feed.

Embodiment 10. The composition of any of the foregoing embodiments, comprising a single strain of the genus Bacillus.

Embodiment 11. The composition of any of the foregoing embodiments, comprising a mixture of strains of the genus Bacillus.

Embodiment 12. The composition of any of the foregoing embodiments, wherein the spore-forming strain of the genus Bacillus inhibits the growth of one or more bacteria selected from a group consisting of Aeromonas hydrophila, Edwardsiella ictaluri, Edwardsiella tarda, Flavobacterium columnare, Streptococcus iniae, and Yersinia ruckeri.

Embodiment 13. The composition of any of the foregoing embodiments, wherein the spore-forming strain of the genus Bacillus inhibits the growth of the oomycete fungus Saprolegnia.

Embodiment 14. The composition of any of the foregoing embodiments, further comprising a bacteriophage that infects E. ictaluri.

Embodiment 15. The composition of embodiment 14, wherein the bacteriophage is φeiAU.

Embodiment 16. The composition of any of the foregoing embodiments, further comprising an agent selected from a group consisting of sulfadimethoxine, ormetoprim, and florfenical.

Embodiment 17. The composition of any of the foregoing embodiments, further comprising an attenuated strain of E. ictaluri.

Embodiment 18. The composition of any of the foregoing embodiments, wherein the spore-forming strain of the genus Bacillus is susceptible to one or more antibiotics selected from a group consisting of carbenicillin, ampicillin, spectinomycin, oxacillin, vancomycin, cephalothin, novobiocin, sulfadiazine, amikacin, erythromycin, neomycin, penicillin, chloramphenicol, sulfamethoxazole, norfloxacin, gentamicin and ciprofloxacin.

Embodiment 19. A method for treating or preventing disease in an animal comprising administering the feed composition of any of the foregoing embodiments to the animal.

Embodiment 20. The method of embodiment 19, wherein the animal is an aquatic animal such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp).

Embodiment 21. The method of embodiment 19 or 20, wherein the disease is enteric septicemia.

Embodiment 22. A microbiocidal composition formulated for administering to an aquatic environment and comprising an effective amount of a spore-forming strain of the genus Bacillus for treating or preventing enteric septicemia.

Embodiment 23. The composition of embodiment 22, wherein the aquatic environment is an environment where aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) are raised.

Embodiment 24. A method of treating or preventing enteric septicemia in aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) comprising administering the composition of embodiment 22 to the environment where the aquatic animals such as farmed fish (e.g. catfish or tilapia) and crustaceans (e.g., shrimp) are raised.

EXAMPLES

The following examples are illustrative and are not intended to limit the claimed subject matter.

Example 1 Biological Control of Channel Catfish Disease

Introduction

Proposed is research that has great potential to improve the environmental sustainability and economic viability of commercial production of channel catfish (Ictalurus punctalus) in the Southeastern United States. Enteric septicemia of catfish (ESC), caused by Edwardsiella ictaluri, and other bacterial and fungal pathogens (e.g., Aeromonas hydrophila, Flavobacterium columnare, and Saprolegnia spp.) are responsible for millions of dollars of losses to the catfish industry annually. For the aquaculture producer, the use of beneficial microorganisms for biological control of disease has the expected advantages of 1) low application costs, 2) no detrimental impact on other bacteria, the environment, or human consumers, and 3) expected synergy between biological control and existing disease control strategies.

This research will ultimately benefit catfish producers by providing them an alternative strategy to control pathogens that affect catfish, thus facilitating more efficient production and making a positive impact on the economic lives of aquaculture farmers in rural southeastern states. Furthermore, by decreasing or eliminating the need for antibiotic (or other chemical) treatment of aquaculture ponds, biological control may lessen the adverse environmental impacts of aquaculture production. Environmentally friendly and cost-effective technology with the ultimate objective of applying biological control agents to decrease the incidence and severity of disease in aquaculture ponds is desirable.

The culture of channel catfish has been one of the most successful animal production industries in North America in the past 30 years, and currently represents the largest aquaculture industry in the United States. In 2009, more than 210 million kg of catfish were processed representing over $360 million in gross farmgate sales. Over 90% of all catfish are produced in Alabama, Arkansas, Louisiana, and Mississippi and are primarily grown in earthen ponds ranging in size from 2 to 10 ha (USDA, Part I: Reference of Fingerling Catfish Health and Production Practices in the United States, 2003; USDA, Part II: Reference of Foodsize Catfish Health and Production Practices in the United States, 2003). Catfish farmers typically stock fish at high densities and use culture systems where environmental conditions can change very rapidly. These adverse conditions place added stress on the fish, creating favorable conditions for the onset and spread of different catfish diseases. As a result many diseases have emerged and become endemic in the catfish industry. The most important of these endemic infectious diseases is ESC, resulting in losses in over 78% of all operations with outbreaks being reported in 42% of foodfish production ponds (USDA, Part I: Reference of Fingerling Catfish Health and Production Practices in the United States, 2003; USDA, Part II: Reference of Foodsize Catfish Health and Production Practices in the United States, 2003). The combination of increased feed prices and high disease incidence is resulting in economic hardship for channel catfish producers.

E. ictaluri is a rod-shaped, Gram-negative bacterium that is highly host-specific for channel catfish (Plumb, 1999). The economic impact of this bacterium in the catfish industry has dramatically risen since first described as the causal agent of ESC in 1981 (Hawke et al., 1981). Today, it is estimated that ESC costs the catfish industry between $20 and $30 million yearly in direct fish losses (Delbos et al., 2001). Enteric septicemia occurs in acute, sub-acute, and chronic forms in channel catfish (Hawke et al., 1981). Fish with ESC are listless and often swim in slow, erratic spirals at the surface of the water. As the disease progresses hemorrhages and ulcers appear along the flanks and back of the fish. In chronically ill fish, an open lesion may develop on the top of the head, giving the disease its common name, ‘hole-in-the-head disease’.

A. hydrophila is also a Gram-negative bacterial pathogen, which has a broader host range than E. ictaluri by causing a hemorrhagic septicemia in all freshwater fish worldwide (Cipriano et al., 1984; Ford et al., 1991). Losses due to A. hydrophila infections are typically of a much smaller magnitude than those due to E. ictaluri and it is often considered a secondary pathogen associated with stress, handling or opportunistic infection (Plumb, 1999); however, a 2009 epidemic of A. hydrophila infections among Alabama catfish producers has been unparalleled in its virulence and rapid dissemination among catfish Biological control of channel catfish disease ponds (Terhune, Liles, et al., manuscript in preparation). Outbreaks of this new A. hydrophila strain have been documented on 48 farms in West Alabama and caused an estimated loss of 3.8 million pounds of fish, primarily harvestable size animals where production costs inputs have already largely been made (W. Hemstreet, personal communication, Alabama Fish Farming Center, Greensboro, Ala.).

Young-of-the-year catfish are most susceptible to ESC and other pathogens. Outbreaks on fingerling operations generally begin in late August or September when the water temperatures decrease from peak summer temperatures to a range conducive for E. ictaluri growth (22-28° C.). Once fish have survived an initial infection, fish can become immune to subsequent infections due to response by the acquired immune system (Klesius, 1992). Usually ponds managed for the production of food-size fish are restocked with fingerlings multiple times during a production cycle to allow for continuous harvesting of the ponds. Hence, foodfish production ponds usually contain a mix of fish with different ages and immune status. Most of the adult fish in a foodfish pond have already experienced a disease outbreak and are immune to the disease but a proportion of them will be carriers of the agent (Klesius, P. H. 1992). Therefore, when naïve fingerlings are stocked in foodfish ponds they are exposed to the agent in the pond environment making them more prone to disease outbreaks (Wise et al., 1998).

Initial efforts to control ESC, A. hydrophila, and other bacterial pathogens were based on feeding antibiotic medicated feed. For the last 20 years, the only antibiotics labeled by the U.S. Food and Drug Administration (FDA) for controlling ESC and Aeromonas infections were Romet® (ormethoprim-sulfamethoxine) and Terramycin® (oxytetracycline), respectively. The FDA recently approved the use of Aquaflor® (florfenical) for ESC outbreaks and it is currently being marketed by the Schering Plough Corp. (Gaunt et al., 2003; Gaunt et al., 2004). However, medicated feed is expensive and usually marginally effective in commercial practice since sick fish may not eat adequate amounts of the medicated feed to clear the infection from the treated population. Additionally, Aquaflor may only be administered with a veterinary feed directive that requires bacterial identification and issuance by a licensed veterinarian that may further delay implementation of corrective treatment actions. The systematic use of antibiotics has also led to the development of bacterial resistance (Khoo, 2001). Recent surveys of catfish ponds in Stoneville, Miss. have shown the presence of a plasmid in E. ictaluri disease isolates that confers resistance to Aquaflor®24.

Most producers have incorporated the use of restricted feeding practices during ESC outbreaks to reduce mortality. However, by reducing feed inputs the growth of fish is sacrificed, severely affecting producers' profits (Wise et al., 1998). Recently, a live, attenuated strain of E. ictaluri has been developed for vaccination purposes and shown limited protection in fingerling channel catfish when vaccinated at 10 days of age, both under experimental and commercial conditions (Lim et al., 2003; Shoemaker et al., 1999; Wise et al., 1998; Wise et al., 2001). However, the vaccine has not been widely accepted by catfish producers since disease often occurs in vaccinated fish populations and the up-front cost can be prohibitive.

With various control strategies in use for catfish disease prevention and yet significant losses still occurring due to pathogens, other complementary approaches may be welcomed by catfish producers. An effective biological control agent would require good efficacy, be very low cost, have potent antibacterial activity, have no adverse environmental impacts, and ideally would enable marketing of catfish as an organically grown product. Biological control agents have recently been identified by the present inventors.

Rationale and Significance

Every animal is a host for a complex microbial ecosystem, with many unique microbial habitats on and within each animal. This complex microbial community can provide protection against disease and aid in the acquisition of essential nutrients. Beneficial microorganisms are being exploited as inoculants in both agriculture and aquaculture, to inhibit pathogens and enhance the health and growth of animal and plant crops. This proposed research will develop Bacillus strains for use in aquaculture, to 1) prevent disease due to bacterial and fungal pathogens, 2) promote sustainable aquaculture practices, and 3) benefit the economic livelihood of aquaculture producers in the State of Alabama.

The use of biological control to prevent and control diseases afflicting agriculture has already been proven to reduce the need for chemical pesticides and antibiotics in food crop production (Kloepper et al., 2004; Lewis et al., 1997; Zehnder et al., 2001). The worldwide use of the insecticidal toxin of Bacillus thuringiensis (Bt) as an alternative to pesticides is one example of the ability of beneficial microorganisms and their natural products to benefit food safety, reduce the reliance on chemical treatment regimes, and foster economically and environmentally sustainable production (Sanchis, 2008). As with agriculture, aquaculture relies upon high density monocrop systems, providing ideal conditions for the growth of pathogenic microorganisms. Antibiotic treatment of farm raised fish and crustaceans leads to an increasing frequency of antibiotic resistant pathogens that can be introduced into human populations, and decreases the market value for farmers forced to depend upon costly chemical methods of disease control. As the demand for quality animal protein sources increases in the 21st century, with probable depletion of wild fish stocks, there is a societal need for environmentally sustainable and cost-effective methods that can be incorporated into aquaculture farming practices (Harlander, 2002; Serageldin, 1999).

The present inventors have demonstrated the efficacy of beneficial bacteria, spore-forming members of the genus Bacillus, to act as biological control agents in preventing disease in plants due to bacterial or fungal pathogens (Kloepper et al., “Theory and applications of rhizobacteria for transplant production and yield enhancement”, 2004; Kloepper et al., “Induced systemic resistance and promotion of plant growth by Bacillus spp.”, 2004; Kokalis-Burelle et al., 2003). In some cases Bacillus strains have also been found to dramatically promote the growth of crop plants and increase plant uptake of soil nutrients (Enebak et al., 1998; Kloepper et al., 2004; Kokalis-Burelle et al., 2003). Spores of Bacillus can be applied to the seeds or roots of plants resulting in a significant decrease in disease symptoms and mortality when the plant is exposed to a pathogen. An extensive collection of Bacillus biocontrol strains useful against plant pathogens (n=160), along with Bacillus cultures isolated from channel catfish intestinal homogenates (n=17), were tested for biocontrol activity against a panel of seven pathogens that are the major causes of aquaculture disease and economic losses worldwide (e.g., FIG. 1). Specifically, each of the bacterial isolates was tested for activity against the bacterial pathogens A. hydrophila, E. ictaluri, E. tarda, F. columnare, Streptococcus iniae, F. columnare, Vibrio harveyi, Yersinia ruckeri, and the oomycete fungus Saprolegnia. Out of this collection of Bacillus strains, the most effective strains for aquaculture use (n=21) have been identified based on their in vitro inhibition of pathogen growth. These 21 Bacillus strains were tested for their ability to survive and grow within the intestine of a channel catfish, by spraying Bacillus spores separately onto catfish feed (˜10⁶ CFU/g feed), feeding aquaria housed catfish fingerlings with the Bacillus-amended feed for one week, then feeding with regular feed for three days, and then sacrificing the animals and estimating the numbers of Bacillus per g of intestinal tissue (FIG. 2). Many of the Bacillus strains achieved high numbers (>10⁸ CFU/g intestine) suggesting that they had successfully colonized the catfish GI tract, whereas seven strains had levels of Bacillus similar to the control group (from indigenous intestinal populations). Ongoing tests will determine the 16S rRNA gene sequences of representative Bacillus colonies recovered from the catfish intestine, to verify that these were the same strains that were introduced to the animals on amended feed.

A “Bacillus cocktail” was prepared by selecting several Bacillus strains and applying Bacillus spores onto catfish feed at approximately equal 10⁵ CFU per strain/g feed. The Bacillus-amended feed was fed to fingerling catfish (n=15 per tank, 5 tanks per treatment group) for two days prior to immersion challenge with 2×10⁵ CFU/ml E. ictaluri strain S97, and then mortalities were recorded over time. A significant decrease in mortality was observed for the catfish fed the Bacillus amended feed, relative to the control group (FIG. 3). This experiment demonstrated that Bacillus spores introduced onto the feed of channel catfish have the ability to reduce disease and mortality in a controlled aquarium model of disease. Together in this proposal these scientists will test Bacillus biocontrol strains for disease control in channel catfish, conducting the critical experiments to develop these Bacillus strain(s) for biological control application.

Despite the promise of probiotic, beneficial microorganisms for disease control, this field of science has been limited by a lack of scientific rigor in evaluating some proposed probiotics, and a need to systematically evaluate many possible biological agents for those that can both be effective and gain regulatory approval. The experiments disclosed herein will 1) identify specific Bacillus strains that may be used for disease control through application onto channel catfish feed, 2) complete a genome sequence for the specific Bacillus strain(s) that show the best promise in disease prevention, 3) determine the structure of the antibiotic(s) produced by each Bacillus strain, 4) perform efficacy studies on the ideal dose and timing for Bacillus administration, and 5) evaluate catfish health after long-term feeding with Bacillus amended catfish feed. For this study, the Bacillus strains are being selected through rational evaluation of their relative efficacy in disease prevention, and for the specific criteria above that are important for their successful use for channel catfish production.

Approach

Testing of the Relative Benefit of Each Bacillus Strain for Control of ESC.

Controlled experimental infections in aquaria will be used to assess bacterial biological control for each specific bacterial strain. Several variables will be assessed in establishing the protective effect of bacterial cultures for their respective biological control activity. Since long term ambient storage may be a requirement for commercial application, endospore forming bacteria within the genus Bacillus have been selected for evaluation for their biological control potential. Of the 15 Bacillus cultures that 1) express robust inhibitory activity against multiple aquaculture pathogens (e.g., FIG. 1), and 2) can survive and replicate within the catfish intestine (FIG. 2), these will be screened separately to identify the most effective strains for in vivo protective effect against ESC in aquaria challenges. Each Bacillus culture will be grown on a sporulation medium for 48 hours and then bacterial cells will be removed with a sterile cotton swab and suspended in sterile water within a 50 ml conical tube. After washing twice with sterile water, the spore suspension will be tested for viable colony forming units (CFUs), and then used to coat catfish feed with approximately 10⁷ bacterial CFU/g feed by spraying a spore suspension at a dose of 8% (v/w). The bacteria coated feed will be dried prior to feeding the catfish. Bacillus spore-coated feed will be stored at 4° C. prior to feeding and is anticipated to be highly stable for long-term (months) storage due to endospore formation.

Assessment of Individual Bacillus Strains to Prevent ESC in Controlled Aquarium challenge.

In these challenge experiments, four aquaria per Bacillus strain, or control group, with 15 fingerling specific-pathogen-free catfish per aquarium will be used. One week prior to challenge, catfish feed coated with specific Bacillus strains will be fed to the fingerling catfish to satiation one time per day, with control tanks receiving sterilized bacterial cells (by autoclaving), or no bacterial addition. For the challenge assay, log-phase E. ictaluri cultures at approximately 10⁵ CFU per ml will be added to the aquaria under static conditions. Fish survival will be monitored daily with end survival rates in each of the treatments used to assess the ability of each Bacillus strain to prevent development of ESC. Control tanks will receive viable bacteria amended feed but will not receive E. ictaluri to verify that there is no detrimental effect of the Bacillus on catfish viability.

Characterize the Antibiotic Compound(s) Produced by Each Bacillus Strain.

Each of the antibiotic-producing Bacillus strains has been found to secrete an inhibitory compound(s) into their growth medium. Cell-free supernatants of Bacillus strains grown either in an M9 minimal medium, or in a complex tryptic soy broth medium, have antibiotic activity against the pathogens previously tested in a cell-based bioassay (e.g., FIG. 1). Identification of the antibiotic compound(s) produced by Bacillus strains will be very important for eventual regulatory approval for use of these strains, either solely or in combination, for disease control.

Partially Purify the Antibiotic by Liquid Chromatography (LC).

The compounds will initially be purified using size exclusion and reverse phase LC and tested utilizing the bioassays disclosed herein. The partially purified compounds will be exposed to different organic extraction and phase separations to determine conditions for rapid extraction from spent media. After defining these conditions, the purification will proceed using the defined C18 retention index as a ‘final’ purification step. The strategies will endeavor to achieve rapid purification of the bioactive compound, restricting the purification to a three-stage protocol when possible.

Many drug synthesis pathways produce more than one product. In addition to inactive compounds, these can include chemically related antibiotics with varying potencies and spectra of activities. For instance, the bacterium that produces epothilone, a candidate anticancer agent, secretes chemically similar epothilones A, B, and D into its medium (Tang et al. 2000). Co-occurring drug-like molecules such as these can be separated by LC as multiple peaks of activity among the fractions. The initial LC partial purification step will separate active compounds and characterize each individual compound's spectrum of antibiotic activity. Purification of individual components to homogeneity will greatly enhance the prospect of successful downstream mass spectroscopy (MS) analyses.

Three types of antibiotic molecules might be obtained: small peptides, organic molecules, or lipids. Size exclusion and C18 chromatography will be able to separate these classes. Failure to be retained on C18 may necessitate additional chemistries be attempted; however, in initial screens of Bacillus antibiotics, we will favor those UV-active compounds that appear to be monodisperse in initial purifications. Variation in the solvent systems and pH will be used to enhance the separation of complex mixtures, while the bioassays disclosed herein provide a powerful tool to monitor integrity of our molecules. The active compounds that can be purified in quantities will be analyzed for structural information by LC/MS. Many potential hurdles can impede compound purification. Some biological activities are due to multi-subunit molecules, which may lose activity when the components are separated by chromatography (e.g., violacein). Additionally, solvation and other treatments during LC may inactivate some molecules. To discern between these two options, different chromatography fractions can be combined and tested for the return of activity.

Chemical Characterization of the Active Compounds.

Chemical characterization of the active compounds will be attempted using thin layer chromatography and MS analysis. Thin layer chromatography (TLC) will be used as an inexpensive strategy to study the homogeneity of the final compound (e.g., monitoring with UV, sulfuric acid charring) and the chemical functionalities (e.g., Ninhydrin reactivity or acetylation reactions) for the antibiotics produced by Bacillus strains. These initial chemical assays will lay the foundation for complex analysis such as MS and NMR. The LC/MS conditions will also permit circumvention of any potential ion suppression that may be present in the mixed samples. Further LC/MS experiments will also be valuable in the refinement of the purification strategies. Additional LC/MS/MS and accurate mass experiments will be performed to sort compounds into groups with structural similarities. Structural data from a single round of LC/MS/MS is often insufficient to completely determine molecular structures. Nonetheless, the data can be matched to literature values to identify previously described compounds. Even incomplete structural data can be used to predict solubility and stability, and determination of molecular weights enables production of solutions at known molar concentrations. The ability to prepare known concentrations of antibiotic compounds is important for determining potency and cytotoxicity. Chemical structure analyses will be performed. Preliminary LC/MS data will aid in the active molecule structural determination. Extraction and chemical analysis to discover structures of the product molecules are relatively expensive processes. To conserve the project budget, complete chemical structure analyses will be performed only for a small number (e.g., <6) of highly active antibiotic compounds that have passed the previous evaluations, and corresponding to Bacillus strains identified as having significant biological control activity. Promising candidate molecules from each structural similarity group will be further characterized using the full set of spectroscopic techniques (UV-vis, UV-vis-NIR, FT-IR, FT-Raman, GC-FTIR, resonance Raman, and NMR spectroscopy). In the initial phase, one-dimensional ¹H and ¹³C NMR (at natural abundance) experiments and multi-dimensional NMR ¹H-¹³C (at natural abundance) Heteronuclear Single Quantum Coherence (HSQC) experiments will be performed to categorize compounds. Full NMR analyses may also be performed.

Determined Relative Potency of Antibiotic Compounds Against Different Pathogens.

Absolute and relative potency data may be utilized to rank compounds for their potential as antibiotics. Each of the bacterial and fungal pathogens tested previously (n=7, see above) will be exposed to dilution series of purified antibiotic compound(s) to determine Minimum Inhibitory Concentrations (MICs). Purified compounds and molecular weight data from LC/MS structural analyses will be used to dissolve compounds to known concentrations. Standard antibiotic assay conditions and media (cation-adjusted Mueller-Hinton broth, when appropriate) will be employed to assess antibiotic potency. Briefly, bacterial cultures in the log phase of growth will be inoculated with a wide range of antibiotic concentrations, in triplicate, and growth inhibition will be determined relative to the negative control (solvent or buffer used for antibiotic compound). Growth kinetics will be determined for each bacterial species for calculation of MIC₅₀ (50% growth inhibition), and the potency of each compound will be compared relative to other known antibiotic compounds. Positive controls will include antibiotics of different classes with previously defined potencies.

Sequence the Genome of the Most Effective Bacillus Biocontrol Strain(s).

The Bacillus strains identified by the experiments herein may be sequenced. The DNA sequence information obtained may be utilized to begin DNA-based strain-specific tracking systems for monitoring the movement of introduced beneficial strains in the environment. In addition, this work will provide an extensive genetic inventory of the biosynthetic pathways involved in natural product synthesis and indicate the metabolic and enzymatic capabilities of each strain, enabling future work to use these genome sequences to assay for Bacillus global gene expression and to enhance antimicrobial biosynthesis during biological control.

Genome Sequencing and Assembly of a Bacillus Strain.

The genome size of each prospective Bacillus strain will be estimated by pulsed field gel electrophoresis (PFGE). Most Bacillus genomes are 4 to 7 Mbp, so using a next-generation sequencing approach can easily generate 50× fold coverage of a Bacillus genome. A combined approach using both 454 pyrosequencing for >30× genome sequencing coverage (˜500 bp read lengths), and >50× genome sequencing coverage using illumina sequencing (˜70 bp paired end read lengths) is an optimal strategy for de novo bacterial genome sequencing. Bacillus cultures will be grown in large scale (500 ml) for DNA extraction, and the genomic DNA will be prepared as a barcoded sublibrary and sequenced. By using a ½ plate 454 format, a sufficient degree of sequencing coverage should be obtained for a single Bacillus genome. The genome sequences will be assembled into a contiguous genome. A bioinformatics software package, CLC Bio Genome Workbench will be utilized to perform high-throughput de novo genome assembly and annotation. In particular, the genome analysis will attempt to identify genetic pathways involved in antibiotic synthesis, and scanning the genome for evidence of any gene(s) potentially involved in pathogenesis (e.g., hemolysins, toxins). A list of predicted open reading frames (ORFs) will be identified using a hidden markov model trained on other completely sequenced Bacillus genomes. The database of Bacillus ORFs will be compared to the GenBank nr/nt database by BLAST algorithm searches, and a preliminary annotation prepared according to the top GenBank hit for each respective ORF. The complete (or nearly complete) Bacillus genome will be a valuable resource for future gene mining and gene expression experiments to support extramural funding opportunities.

Generation of Bacillus Mutants that Lack Antibiotic Synthesis.

To identify the specific gene(s) required for antibiotic synthesis, a Mariner transposon system (Wilson et al., 2007) will be used to randomly transposon mutagenize the Bacillus strains (n=3) that will be selected for complete genome sequencing. The Bacillus Tn mutants will encode spectinomycin resistance, and each mutant colony will be overlayed with soft agar (0.7%) containing a log phase culture of E. ictaluri. Each of the mutants that lack a zone of inhibition will be selected for further study. It will be possible to very rapidly screen tens of thousands of mutants for loss-of-function in this manner, providing an exhaustive collection of antibiotic-deficient mutants. Each of the mutants will be compared by Southern blot analysis using a probe targeting the transposon cassette, thereby indicating mutants with a transposon insertion in the same (or immediately adjacent) genetic locus. Every unique mutant will be tested against a wider panel of bacterial and fungal pathogens described above, to determine if the loss-of-function for an antibiotic that inhibits E. ictaluri growth is similarly lacking for the other pathogens. It may be the case that a Bacillus strain could express multiple antibiotics, in which case different pathogens may be used for the primary screen in order to identify a loss-of-function mutant deficient in antibiotic synthesis.

To identify the gene(s) required for antibiotic synthesis, the genomic DNA of unique mutants will be extracted and used as template for inverse PCR using primers internal to the transposon cassette to identify the Bacillus gene(s) adjacent to the site of transposon insertion. The DNA sequences will be compared to the complete Bacillus genome sequence (as the reference genome) to indicate the relative location of each transposon insertion within the genome. This will be critical information to understand the genetic pathway(s) involved in synthesis of an antibiotic that can impair the growth or viability of E. ictaluri and other pathogens. By using multiple Bacillus strains for biological control, this is in effect using a multi-drug formulation, thereby reducing the likelihood of drug-resistant pathogens. It would also be of interest to test whether a Bacillus mutant lacking antibiotic synthesis would be impaired in its biological control activity, compared to its wild-type parent strain.

Develop the Optimal Formulation of Bacillus Strains for Biological Control of Disease.

The choice of the optimal Bacillus strain, or combination of strains, for biological control of disease may be informed by many different sources of experimental data. This proposed research will identify the optimal Bacillus strain(s) and conditions of for control of ESC.

Bacillus Dose-Dependence.

In the first of these experiments to evaluate each strains' ability to control disease in vivo, four of the best Bacillus strains identified above as preventing E. ictaluri infection and mortality will be used to determine the best dose to incorporate into feed for administration. Bacillus spores and feed preparation will be performed as described above; however, the number of spores incorporated into the feed will be altered. The doses will comprise 10⁴, 10⁵, 10⁶, or 10⁷ CFU/g of feed plus a control treatment. Fish will be placed into challenge aquaria (as described above) divided into treatments (with five replicate aquaria per dose) and fed treatment feed daily to satiation, with feeding of the treated feed continuing for 2 weeks. Fish will be challenged under static immersion as described above. Fish will not be fed on the day of challenge, but will resume feeding one day post-challenge and continue throughout the challenge study with the assigned treatment feed. Mortalities will be monitored for at least 21 days. Each Bacillus strain will be evaluated separately.

Bacillus as a Prophylaxis or a Cure.

In a second series of experiments, Bacillus strains will be tested with respect to prophylactic and/or ability to eliminate ongoing infections. These tests will be performed via altering the time at which the spores are initially fed to fish in relation to the timing of challenge. For each Bacillus strain identified and utilized above, four initiating times will be evaluated plus a control group. Fish will be stocked into challenge aquaria as described above and randomly assigned into one of five treatments: 1) Bacillus-amended feed started 1 week prior to challenge, 2) Bacillus-amended feed started 3 days prior to challenge, 3) Bacillus-amended feed initiated 1 day post-challenge, 4) Bacillus amended feed initiated the day of the first E. ictaluri related mortality (based on clinical and behavioral signs), and 5) control feed. All treatment groups will be fed Bacillus-amended feed throughout the experiment with feed amount being offered to satiation. Feed preparation and challenge protocols will be conducted as described above.

Growth and Pathology Related to Bacillus Administration.

Based on the dose of Bacillus identified above, catfish will be subjected to a growth performance trial with each of the four best identified bacterial strains and their respective best dose. Feed will be prepared as previously described with the appropriate Bacillus dose. Juvenile fish (˜5 g each) will be counted, weighed collectively, and placed into aquaria and randomly assigned the designated feed treatment with four replicate aquaria per treatment, 16 fish per replicate tank. Fish will be fed one time daily with approximately 4-5% body weight (approximate satiation; based on initial weight) with prepared feed. Feed will be weighed daily. Every two weeks for eight weeks, all fish will be removed from the tank weighed collectively and weight used to adjust amount of feed offered. At weeks four and eight, four fish from each tank will be removed from each tank. A section of the lower intestine will removed and used to assess the number of desired Bacillus organisms (CFU/g) inhabiting the tissue. The remaining fish tissues will be preserved in 10% neutral buffered formalin for histopathological evaluations. Final weights of the fish will be used to determine growth performance impacts and feed conversion rates.

Combinations of Different Bacillus Strains (“Cocktails”) for ESC Biological Control.

Use each Bacillus strain, at its ideal dose, in every possible combination to assess each Bacillus “cocktail” for its potential in controlling ESC disease. Treatment feeds will be prepared as previously described with equal spore doses of one to four Bacillus strains. Fish challenge experiments will be conducted as described above, utilizing five replicate aquaria per cocktail treatment with 15 fish per replicate. Fish will then be fed the appropriate treatment feed for one week prior to challenge and then continuously post-challenge for the duration of the experiment.

Example 2 Identification of Bacillus Strains for Biological Control of Catfish Pathogens

In the following Example 2, research proposed and completed in Example 1 was further performed and replicated.

Abstract

Bacillus strains were selected and evaluated for biological control of disease in catfish. Bacillus strains were isolated from soil or channel catfish intestine and screened for their potent antagonism against Edwardsiella ictaluri and Aeromonas hydrophila. Twenty one strains were selected and their antagonistic activity against other aquatic pathogens was also tested. The survival of each Bacillus strain in the channel catfish intestine was determined, and five Bacillus strains with the best spectrum of antimicrobial activity and intestinal survival were further evaluated for their protective activity against E. ictaluri challenge in replicate aquaria. Two Bacillus strains conferred significant benefit in reducing catfish mortality (P<0.05). A similar challenge experiment conducted in Vietnam with four of the five Bacillus strains also showed protective effect against E. ictaluri in striped catfish. Safety study in three of the selected strains did not show presence of plasmids and resistance to clinically important antibiotics. Bacillus strains were beneficial to catfish when administered as a feed supplement for the control of diseases caused by E. ictaluri. The Bacillus strains selected in this study have potential application in aquaculture as a cost-effective alternative to the current use of antimicrobial compounds.

Introduction

Aquaculture farming of the channel catfish, Ictalurus punctatus, has been one of the most successful animal production industries in North America in the past 30 years and currently represents the largest aquaculture industry in the United States. Over 90% of all catfish produced in the U.S. are raised in Alabama, Arkansas, Louisiana, and Mississippi and are primarily grown in earthen ponds ranging in size from 2 to 10 ha (USDA 2003a, 2003b). Catfish farmers typically stock fish at high densities.

High feed inputs associated with high density fish culture stimulate the proliferation of opportunistic bacteria (Austin et al. 1995). Also, the high fish density and rapidly changing temperature and chemical composition of aquaculture ponds place stress on the fish, creating favorable conditions for the onset and spread of disease. Enteric Septicemia of Catfish (ESC), caused by the Gram negative bacterium Edwardsiella ictaluri (Hawke 1979), is the most important endemic infectious disease in the channel catfish aquaculture industry (Hawke and Khoo 2004). Losses resulting from ESC were reported in over 78% of all operations with outbreaks being reported in 42% of catfish production ponds, with an economic loss between $20 and $30 million yearly (Wagner et al. 2002; USDA 2003a, 2003b).

Another important pathogen in channel catfish is Aeromonas hydrophila, which is the primary causative agent of motile aeromonad septicaemia (MAS) (Harikrishnan et al. 2003) and can infect multiple fish species including tilapia, catfish, goldfish, common carp, and eel (Pridgeon et al. 2011). In 2009 and 2010, A. hydrophila was identified as the etiologic agent of a disease epidemic in farmed channel catfish, resulting in higher mortality rates than typical for MAS with over 5 million pounds of catfish lost in the Alabama commercial catfish industry. The A. hydrophila strains (e.g., strain AL09-119) isolated from diseased fish during this epidemic are highly virulent in aquaria disease challenge trials compared to A. hydrophila reference strains (Pridgeon et al. 2011).

Pangasianodon hypophihalmus Sauvage, commonly known as the striped catfish, is the native catfish in the Mekong Delta of Vietnam. The farming sector of P. hypophthalmus has recorded the highest growth rate in volume compared to any other aquaculture commodity globally over the last decade (Phan et al. 2009; Phuong and Oanh 2009). The sector accounted for 687,000 and 1,094,879 t production, in 2007 and 2008, respectively, the latter amounting to 34% of the total aquaculture production in Vietnam, the fifth-ranked nation in global aquaculture production (De Silva et al. 2010). Furthermore, over 90% of the farmed catfish is processed and exported to more than 100 countries globally (Phuong and Oanh 2009). Bacillary necrosis of Pangasius spp. (BNP), also caused by E. ictaluri, is an economically significant disease for striped catfish aquaculture industry in the Mekong Delta, which can cause 50-90% mortality and occurs in 98% of farms (Phan et al. 2009).

Chemotherapy by oral administration of antibiotics in fish feeds is the most common treatment for bacterial diseases; however, the use of antibiotics in aquaculture may introduce potential hazards to public health and to the environment by the emergence of drug-resistant microorganisms and antibiotic residues (Johnson 1991; DePaola et al. 1995; Plumb et al. 1995). Furthermore, the normal commensal microorganisms in the digestive tract, which contribute to fish health and nutrition, are inhibited by oral chemotherapy (Gerald and Jane 1966; Sugita et al. 1990). In order to rectify this situation, greater emphasis has been placed on improved husbandry through better nutrition, improved water quality, lower stocking densities, and the use of vaccines and non-specific immunostimulants (Austin and Austin 1999). Few studies have been conducted to investigate probiotic bacteria for mitigating infectious diseases in channel catfish, and no studies have been reported using direct administration in feed. Queiroz and Boyd (1998) applied a commercial probiotic product, Biostart, which contained a few species of Bacillus spp., to channel catfish pond water and demonstrated that survival and net production of fish treated with Bacillus spp. were significantly greater than the control. However, the bacteria used in this previous research were not isolated specifically for use in channel catfish nor were their antimicrobial activity against important pathogens of channel catfish characterized.

In this research an extensive collection of Bacillus strains (n=160) isolated from soil and strains from the intestine of channel catfish (n=17) was tested for in vitro antimicrobial activity against E. ictaluri strains isolated from diseased catfish, A. hydrophila, and other bacterial and fungal pathogens of channel catfish. Bacillus strains that showed effective antibiosis were evaluated for their respective survival in the intestine of channel catfish. The biological control activity of the best performing Bacillus strains when amended onto feed was investigated using channel and striped catfish disease challenge studies in an aquarium system. The safety of selected Bacillus strains was also assessed in terms of the presence of plasmids and resistance to antibiotics.

Material and Methods

Bacterial Strains.

E. ictaluri strain S97-773 was used for the primary screening for Bacillus antibiosis and for ESC challenge experiments since this strain is highly pathogenic for channel catfish and has previously been used in challenge studies at Southeastern Cooperative Fish Disease Laboratory (SCFDL), Auburn University. E. ictaluri strain R-4383, E. ictaluri strain Alg-08-200, Edwardsiella tarda, Streptococcus iniae, Yersinia ruckeri, Flavobacterium columnare, and Saprolegnia ferax were from the collection of pathogenic isolates at the SCFDL. E. ictaluri NLF33 were isolated from diseased striped catfish in Vietnam. Aeromonas hydrophila AL09-119 was isolated from a diseased channel catfish with MAS in 2009. The collection of soil-derived Bacillus strains (n=160) was provided by the laboratory of Dr. Joseph Kloepper (Department of Entomology and Plant Pathology, Auburn University). Bacillus subtilis 1E17 was obtained from Bacillus Genetic Stock Centre.

Isolation of Bacillus spp. Strains from the Intestine of Channel Catfish and Evaluation of Antimicrobial Activity.

Healthy catfish (7-10 cm) were killed by administration of an overdose of MS-222, and the digestive tracts were removed in their entirety. Approximately 1.0 g was homogenized in 9.0 ml of sterile saline (0.9% w/v). Ten-fold serial dilutions were prepared to 10⁻⁶ in fresh saline, and 0.1 ml was spread over the surface of triplicate plates of tryptone soy agar (TSA) with incubation at 28° C. for 48 h (Irianto and Austin 2002). Bacillus-like colonies were picked at random, purified by streaking for isolated colonies on fresh media, and examined for inhibition against the growth of E. ictaluri using the double-layer soft agar method (Jack et al. 1996). For the soft agar overlay, the bacterial isolates were grown in 5 ml of tryptone soy broth (TSB) for 24 h at 30° C. A volume of 5 μl was then spotted onto triplicate plates of TSA and incubated for a further 24 h. Soft agar (0.7% w/v agar) prepared with TSB was melted and cooled to 37° C. and seeded with an inoculum of log-phase E. ictaluri strain S97-773 to achieve slight turbidity (i.e., 10⁷ cells/ml). The bacterial cell suspension in soft agar was immediately poured over the TSA plates and incubated for 24 h at 30° C. whereupon the presence of zones of clearing in the growth of the lawn of E. ictaluri were recorded (in mm) as evidence of growth inhibition. Cultures that were regarded as inhibitory to E. ictaluri were characterized by Gram staining and 16S rRNA gene sequencing using the ‘universal bacteria’ primer set 27F and 1492R (Weisburg et al. 1991). A consensus 16S rRNA sequence was produced using Chromas Pro (Technelysium Pty Ltd., Queensland, Australia), and each sequence was compared to the GenBank non-redundant nucleotide database by BLASTn. Bacillus spp. strains were cryopreserved at −80° C. The collection of soil-derived Bacillus strains (n=160) was tested for antimicrobial activity against E. ictaluri using the same method.

Fifty Bacillus strains with antagonistic activity against E. ictaluri S97-773 were tested for their inhibitory activity against other E. ictaluri strains (E. ictaluri R-483, E. ictaluri Alg-08-200). Bacillus strains that showed antimicrobial activity against all three E. ictaluri strains were evaluated further for their activity to inhibit the growth of A. hydrophila strain AL09-119. Twenty-one Bacillus strains that showed significant antimicrobial activity against both E. ictaluri and A. hydrophila were tested for their activity against several other channel catfish pathogens including Edwardsiella tarda, Streptococcus iniae, Yersinia ruckeri, Saprolegnia ferax with the soft agar overlay method described above.

The antimicrobial activity against Flavobacterium columnare was tested by an agar well diffusion method. For the well diffusion assay, the Bacillus strains were grown in 5 ml of TSB for 48 h at 30° C. After centrifugation at 3,600×g for 10 min, the culture supernatant was filtered through a 0.2 μm filter. Then 200 μl of the filter-sterilized supernatant was added to a round well (approx. 20 mm in diameter) made in a F. columnare growth medium (FCGM) agar plate (Farmer 2004). After the supernatant was absorbed into the agar medium, a log-phase F. columnare culture grown in FCGM broth was spread thoroughly over the plate using a sterile cotton swab. The plates were incubated for 48 h at 30° C.

Bacillus strains AP79, AP143, AP193L, AP254L, and AB01 were also tested for their in vitro antimicrobial activity against E. ictaluri NLF33, the causative agent of BNP in striped catfish. A broth culture of E. ictaluri was adjusted to 10⁶ CFU/mL and evenly swabbed onto TSA plates. Three wells were punched from the agar plate and 50 μL of a 10⁸ CFU/mL of a Bacillus cell-free supernatant (48 h culture in TSB) was added into each well. Zones of inhibition were measured after 24 hours incubation at 30° C.

Bacillus Genome Sequencing.

Bacillus strain genomic DNA was extracted from 500 ml cultures grown in TSB using the Promega genomic DNA isolation kit (Madison, Wis.). The yield and purity of the genomic DNA were estimated using a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, Del.), and approximately seven micrograms of Bacillus genomic DNA was sent to the Lucigen Corporation (Middleton, Wis.) for bar-coded sub-library generation for 454 pyrosequencing with titanium chemistry. Bar-coded Bacillus sub-libraries were sequenced at the Genomic Services Lab at Hudson Alpha (Huntsville, Ala.) using a Roche 454 Genome Sequencer FLX (Branford, Conn.) with either two Bacillus genomes per one-half 454 plate (strains AP143 and AP 254L) or three Bacillus genomes per a full 454 plate (strains AP18, AP193L, and another strain not described in this study). The genome sequences were imported into the CLC Genomics Workbench (Cambridge, Mass.), trimmed for quality at 0.01 stringency, and de novo assembled using assembly settings of length fraction=0.5 and similarity=0.8. The collection of contiguous genome sequences (contigs) larger than 10 kb was exported into a FASTA formatted file, and each contig was compared to the GenBank nr database by BLASTn. In addition, the open reading frames (ORFs) on each contig were predicted with the GeneMark.hmm for Prokaryotes program, which used the B. subtilis ORF-finding model. The predicted ORFs for each Bacillus genome were compared to the sequences in the nr database at GenBank by BLASTn and BLASTx. The percent identity of the Bacillus genome sequences to known Bacillus genomes in the GenBank database was estimated by including the BLAST results of all contigs greater than 10 kb together and assessing the cumulative percent identity for all contigs against specific Bacillus genomes for the respective aligned genome regions divided by the total number of sequenced base pairs within these contigs. In this way, the species designation for each of the sequenced Bacillus strains was determined and is indicated in Table 1, with % identity values of greater than 70% indicative of a species affiliation.

Preparation of Bacillus Spores and Spore-Amended Feed.

Bacillus spores were prepared by the method described by Kenny and Couch (1981) with some modifications. Bacillus strains were grown in TSB at 30° C. overnight. Then the broth was spread on spore preparation agar (peptone 3.3 g/l, beef extract powder 1.0 g/l, NaCl 5.0 g/l, K₂HPO₄ 2.0 g/l, KCl 1.0 g/l, MgSO₄.7H₂O 0.25 g/l, MnSO₄ 0.01 g/l, lactose 5 g/l, agar 15 g/l) by a sterile cotton swab and incubated at 28° C. for 5 to 7 days. To collect the spores, 5 ml of sterile distilled water was added to the plate and the spores were suspended in water using an inoculation loop. The spore suspension was then incubated at 85° C. for 15 min to kill the vegetative cells. The concentration of the spore suspension was determined by serial dilution and spreading onto TSA. The final concentration of the spore suspension was manipulated with sterile water to 1.25×10¹⁰ CFU/ml for the intestinal survival assay and 10⁹ CFU/ml for the ESC challenge study. To prepare spore-amended feed, 80 ml of the spore suspension was sprayed onto 1000 g commercially available slow-sinking pelleted fish feed (2 mm, 40% protein, Zeigler, Gardners, Pa.) using a bleach- and ethanol-sterilized pump sprayer to achieve approximately 8% v/w spore suspension application. The feed was then mixed thoroughly with 30 ml fish oil. The control feed was ammended solely with fish oil.

Inoculation and Quantification of Bacillus spp. in the Intestine of Channel Catfish.

Fingerling channel catfish (7-10 cm) were distributed into twenty-two 60 L tanks each containing 15 L water and three fish. Fish were starved for one week prior to the experiment. Catfish feed was amended in separate batches with the 21 Bacillus strains that showed good antimicrobial activity against both E. ictaluri and A. hydrophila using the spore application method described previously. Each unique Bacillus strain-amended feed (˜10⁹ CFU/g feed) was given to one aquarium tank. The fish were fed once daily with spore-amended feed or control feed for one week, and thereafter all fish received the control feed for three days. One tank was used as the control and received untreated fish feed for the duration of the experiment. Daily feeding rate was 3% of total body weight.

At the end of the experiment, all of the fish were killed by administration of an overdose of MS-222. The intestine was removed, weighed, and then homogenized in 2 ml of sterile saline (0.9% w/v). Homogenized samples were then serially diluted in sterile saline and spread on TSA and incubated at 28° C. for 48 h. Three representative colonies with the same morphology as the applied Bacillus strain were randomly picked from the plate, purified on new plates and identified by 16S rRNA gene sequencing as described previously and compared with the known 16S rRNA gene sequence from each Bacillus strain. For the control and treatment groups, only the unique colony morphology corresponding to that of the amended Bacillus strains was recorded. Culturable counts for each Bacillus strain recovered from the intestine were determined as CFU/g of intestine sample.

Aquarium Challenge Studies.

Five Bacillus strains (AB01, AP143, AP193L, AP254L, and AP79) were selected for further evaluation in an aquarium challenge trial with E. ictaluri strain S97-773. Five Bacillus treatments and one control each with four replicate aquaria were included. Each replicate aquarium was stocked with 25 fingerling channel catfish weighing about 13 g. Fish were acclimated to commercial dry feed for one week. Fish from each treatment group were then fed with an experimental diet supplemented with spore of a Bacillus strain (8×10⁷ CFU/g) at a daily feeding rate of 2.5% fw/bw (feed weight/body weight) for two weeks. Fish in the control group received normal feed only.

Fish were challenged by immersion for 45 minutes in 10 L of water containing E. ictaluri S97-773. All fish from the same group were immersed in a single container. The concentration of E. ictaluri S97-773 was determined to be 4.5×10⁶ CFU/ml. The challenge condition for the control group was the same as other treatments except that BHI medium was added instead of E. ictaluri culture. Mortalities were monitored over a 21-day period, and dead fish were dissected and the presence of E. ictaluri confirmed by microbiological examination of kidney and liver swabs on TSA. The identity of the recovered E. ictaluri was confirmed by biochemical analysis.

Fish were reared in a recirculating system during the acclimation period. Upon initiation of Bacillus feeding and during the challenge phase, a static system was incorporated with a 20-30 minutes water exchange daily. Sponge biofilters and daily removal of uneaten/waste materials were incorporated to control potential water quality problems. Water temperature was kept at 26±2° C. During the static phase, the central room heating system in conjunction with submersible aquarium water heaters was used to control the required water temperature, and a water heater system was used to control the temperature of the incoming water during water exchange.

Another challenge trial using channel catfish was conducted with a lower dose of E. ictaluri and flow-through conditions. In this challenge experiment, five Bacillus treatments (AP79, AP143, AP193L, and AB01) and one control each with four replicate aquaria were included. Each aquarium was stocked with 20 fingerling channel catfish (˜12 g). A lower dose of E. ictaluri S97-773 (8×10⁵ CFU/ml) was used to challenge fish and starting immediately after challenge the aquaria were flushed for 5-8 hours a day. All other conditions in this challenge were the same as in the previous one. Mortalities were monitored over a 21-day period after challenge, and presence of E. ictaluri in the dead fish was confirmed as previously described.

An additional challenge trial was conducted to evaluate the protective effect of four Bacillus strains (AP79, AP193L, AP254L, and AB01) against E. ictaluri for striped catfish. Five treatments with four replicate tanks each were included in this study. Each tank was stocked with 18 striped catfish (˜14 g). Striped catfish were administered feed amended with Bacillus spores (˜10⁷ CFU/g feed) and control feed for 2 weeks and the fish were transferred to 80 L tanks for a bath challenge with E. ictaluri NLF33. Fish were immersed for 30 min in static, aerated aquaria at a dose of ˜10⁶ CFU/mL to target about 70% mortality in the control group. The control and test diets were offered throughout the challenge phase. The recording of mortality and confirmation of E. ictaluri in dead fish were conducted as above.

Plasmid Analysis.

Plasmid DNA was extracted from Bacillus strains AP79, AP193L, and AB01, by alkaline lysis method (Birnboim and Doly 1979). Bacillus subtilis 1E17 containing plasmid pC194 was used as a positive control. The extracted DNA was analyzed by a Chef-DR II pulsed field electrophoresis system (Bio-Rad, Hercules, Calif.). Pulse time ranged from 1 to 15 seconds for 15 hours at 6 V/cm. The gel was stained with ethidium bromide and visualized using an AlphaImager HP gel documentation system (ProteinSimple, Santa Clara, Calif.).

Antibiotic Resistance Analysis.

The susceptibility of Bacillus strains AP79, AP193L, and AB01 to carbenicillin, ampicillin, spectinomycin, oxacillin, vancomycin, cephalothin, novobiocin, sulfadiazine, amikacin, erythromycin, neomycin, penicillin, chloramphenicol, sulfamethoxazole, norfloxacin, gentamicin and ciprofloxacin was determined by disc diffusion test following procedures outlined by National Committee for Clinical Laboratory Standards (CLSI 2012). A log-phase culture of each strain was diluted to a concentration of approximately 1×10⁸ to 2×10⁸ CFU/ml (McFarland standard 0.5). The inoculum was then seeded onto a Mueller-Hinton agar plate using a cotton swab. Antibiotic-impregnated discs (BD Biosciences) were placed on seeded plates, and the diameter of the zone of growth inhibition was measured after 18 h of incubation at 37° C. The experiments were repeated three times and the average diameter of inhibition zones was calculated.

Statistics.

Completely randomized design was used in this research. Data were presented as mean±standard error (SE). Challenge data were subjected to analysis of variance in SAS 9.2. Differences between means were tested by Tukey's range test and were considered significant when probability (P) values<0.05 were obtained.

Results

Characterization of Bacillus Isolates.

Each of the Bacillus strains isolated from soil or catfish intestine that exhibited inhibitory activity against both E. ictaluri and A. hydrophila was capable of endospore formation. Each pure Bacillus culture was ribotyped, indicating that most of the Bacillus strains were within the B. subtilis group (inclusive of B. amyloliquefaciens), with two strains of B. pumilus also within the collection. Since B. subtilis or B. amyloliquefaciens isolates cannot be conclusively differentiated based on biochemical or 16S rRNA gene sequence data, in some cases genome sequence data were available (i.e., for strains AP18, AP143, AP193L, and AP254L) and were used for phylogenetic classification. For each of these strains there was >80% identity to the most closely related Bacillus strain genome, providing unequivocal evidence of phylogenetic affiliation. Of the strains selected for genome sequencing, only strain AP193L was selected solely on the basis of its antagonism against aquaculture pathogens and efficacy in reducing mortality due to ESC. A full annotation of these genomes is beyond the scope of this study, but these genome sequences do provide an objective assessment of phylogeny and indicate putative biosynthetic pathways for antimicrobial synthesis that may be relevant to biological control of catfish pathogens (data not shown).

Antimicrobial Activity of Bacillus Strains.

The Bacillus strain AB01 isolated from the catfish intestine showed significant antimicrobial activity against E. ictaluri. From the collection of soil-derived Bacillus strains, 50 strains showed significant antagonism against E. ictaluri. All of the 50 Bacillus strains also showed inhibitory activity against E. ictaluri R-4383 and E. ictaluri Alg-08-200. A total of 21 Bacillus strains showed potent antibiotic activity against both E. ictaluri and A. hydrophila (e.g., FIG. 1). The 21 Bacillus strains selected were tested for their activity against multiple pathogens in aquaculture. All of the strains were antagonistic against multiple catfish pathogens, including Gram-negative and -positive bacteria, and the oomycete Saprolegnia. Bacillus strains AB01, AP193L, AP219, and AP301 showed antimicrobial activity against all of the tested pathogens (Table 1). Also, all of the five tested Bacillus strains (AP79, AP143, AP193L, AP254L, and AB01) showed significant antagonistic activity against E. ictaluri NLF33.

Survival and Persistence of Bacillus Strains in the Intestine of Channel Catfish.

Administered bacteria were recovered from the intestine. Over 10⁷ CFU/g of introduced Bacillus was observed in the gut for strains AB01, AP76, AP77, AP79, AP143, and AP254L (FIG. 4). For strains AP18, AP280, and AP303, the counts of recovered bacteria were relatively low, and they were eliminated from further investigation. None of the 21 Bacillus strains were recovered from the control group. In all cases the 16S rRNA gene sequence determined from representative colonies matched the 16S rRNA gene sequence from the respective Bacillus strain that was added to catfish feed. For some of the Bacillus strains that were observed to have high CFU/g intestinal counts (e.g., strains AB01 and AP76), the only colonies observed at the 10⁻⁶ and 10⁻⁷ dilutions corresponded to the respective Bacillus colony morphology.

Challenge Study.

In the first challenge, the mean mortality of the control group was 98.0%. Treatment groups of Bacillus strains AP143 or AB01 showed significantly reduced mortality compared with the control (P<0.05), with 83.1%, 84.8%, and 79.6% mortality for these strains, respectively. And there is no significant difference among the two strains. The treatment groups of Bacillus strains AP79, AP193L, or AP254L (with mortality 89.0%, 95.0%, and 93.7%, respectively) did not show significant differences compared with the control (FIG. 5A, Table 2). For the second challenge, 41.3% of the fish died in the control group. The mortality in the treatment groups ranged from 35.0% to 46.3% with no significant differences observed between any of the treatment groups and the control (FIG. 5B, Table 2).

In the striped catfish challenge experiment, the treatment group fed strain AP79 spore-amended feed had the lowest (9.7%) cumulative mortality and was significantly different from the control (P<0.05). The treatment group fed strain AP193L-amended feed attained 30.6% mortality; however, it should be noted that most of the mortality was recorded in a single aquarium tank on day 4 of the challenge. Catfish fed with strains AP254L and AB01 had 54.2% and 56.9% mortality, respectively, while the control group had 70.8% mortality (FIG. 5C, Table 2).

Plasmid and Antibiotic Resistance Study.

An analysis of plasmid DNA content for selected Bacillus strains was conducted by PFGE, and we did not observe the presence of any plasmid within these four strains but the positive control did show the presence of plasmid pC194 (data not shown). Evaluation of antibiotic susceptibility determined that all four strains were susceptible to all of the tested antibiotics to varying degrees. They were all highly susceptible to carbenicillin, cephalothin, sulfamethoxazone and ciprofloxacin (>25 mm of diameter of inhibition zone). Ampicillin, penicillin, vancomycin, novobiocin, amikacin, erythromycin, neomycin, chloramphenicol, norfloxacin and gentamicin also inhibited their growth effectively (20-25 mm zone of inhibition), whereas spectinomycin, oxacillin, sulfadiazine showed moderate inhibition (15-20 mm inhibition zone). These four strains showed very similar antibiograms, with the variation of diameters of inhibition zone within the four strains lower than 10% of the average diameter for each of the antibiotics tested.

Discussion

The results of this study indicate that specific strains within the Bacillus subtilis group show promise for disease control in catfish aquaculture. In previous research, application of Bacillus cultures to pond water resulted in improved fish survival and yield (Queiroz and Boyd 1998). However, Bacillus cultures used in the latter study had not been evaluated for antagonism against E. ictaluri or other aquaculture pathogens. Furthermore, the ability of the Bacillus cultures from this commercial product to reduce the mortality or disease symptoms due to ESC was not evaluated and was complicated due to an infection of catfish by proliferative gill disease during the experimental period. This study is the first to select probiotic bacteria for control of ESC and other pathogens in catfish and to evaluate for their biocontrol efficacy via feed administration. Bacillus spp. were used in this research as they could be applied in spore form, thus facilitating easy storage and application, and many of the Bacillus strains had been previously studied for their ability to antagonize bacterial and/or fungal pathogens of plants (Kloepper et al. 2004).

Gatesoupe (1999) concluded that probiotics for aquaculture should be antagonistic to pathogens, colonize intestines, and increase resistance of the host to pathogens. Ideally probiotic bacteria should be selected by considering all three criteria. However, it is difficult to evaluate potential probiotic bacterial strains for the second and third criterion on a large number of candidate bacteria. Therefore, in vitro antimicrobial activity was the primary criteria by which a large number of strains were evaluated, with candidate bacterial strains that did not show antagonistic activity eliminated from further study. The primary objective of this research project was to identify bacterial strains that can be applied for the control of E. ictaluri, A. hydrophila, and other bacterial and oomycete pathogens of catfish. Since the bacterial pathogens E. ictaluri and A. hydrophila are responsible for the majority of the mortality observed currently in catfish aquaculture, the ability of a Bacillus strain to inhibit the growth of these two pathogens was of paramount importance and only the strains capable of inhibiting both pathogens were selected for testing in aquarium disease challenges.

The ability of a probiotic bacterial strain to colonize and survive within or on its host is also an important criterion for strain selection. However, in many cases the probiotic bacteria may not permanently colonize the gastrointestinal tract but instead achieve a sustained transient state (Robertson 2000; Irianto and Austin 2002). Even transient bacteria may be efficient at mediating biological control of disease if the cells are introduced artificially via food either continuously or semi-continuously (Gournier-Chateau et al. 1994; Gatesoupe 1999). High population levels of several Bacillus strains were recovered from catfish intestines three days post-feeding with Bacillus-spore amended feed. For Bacillus strains with high counts in the intestine, colonies with the same morphology as the applied Bacillus strain dominated the TSA plates, and the ribotype of the representative colonies confirmed their identity as the applied Bacillus strain. In a previous study of the persistence of an E. ictaluri-specific bacteriophage within the intestine of channel catfish, it was observed that 72 hours post-feeding the bacteriophage could not be detected within intestinal samples (Carrias 2011). This implies that any inert particle would be cleared from the catfish intestine by 72 hours post-feeding and that bacterial strains detected after this time frame would have some degree of intestinal persistence. Considering that bacterial population levels in the intestine should decline after cessation of feeding with the spore-containing diets, the maximal level of Bacillus strain CFU/g of intestinal tissue reached during the feeding regime may be higher. The bacterial population levels here (10⁶-10⁷ CFU/g for most of the strains) are in general agreement with previous studies involving fish (Jöborn et al. 1997; Gildberg and Mikkelsen 1998; Robertson et al. 2000; Irianto and Austin 2002). These results demonstrate that some of the Bacillus strains evaluated in this study can persist within the catfish gastrointestinal tract for at least three days. However, at this point the degree of persistence and ability to colonize the intestinal mucosa are unknown for each strain. A more detailed experiment evaluating the colonization and/or persistence of specific Bacillus strains within the catfish intestine will be conducted to help understand the biocontrol mechanism(s) of Bacillus strains and guide the duration and timing of Bacillus feeding. Future studies will also examine the impact of each Bacillus strain on the intestinal microbiota and the health and growth of the fish in the absence of aquaculture pathogens.

In one of the ESC challenge studies a very high mortality (98.0%) was observed in the control group, which may have affected the degree of protection that could be afforded by Bacillus strains. Ideally, an aquarium disease challenge would result in a mortality of 60%-70%, which more accurately simulates the natural development of ESC. The high mortality was probably a consequence of maintaining a static system during the challenge, wherein the E. ictaluri persisted in the tank for an extended period of time. Despite the higher mortality observed in this challenge, two Bacillus strains (AP143 and AB01) provided significant protection to channel catfish. It is important to note that the two challenges that showed protective effects for Bacillus strains were in a static system with 20-30 minutes of water exchange daily, while the challenge with no significant effect was conducted in a system flushed for 5-8 h every day after challenge. This suggests that a more pond-like environment wherein the probiotic is maintained within the water, and potentially the skin and gills of the fish, may be more conducive for effective biological control of disease. In addition, presumably at the lower doses of E. ictaluri that catfish are typically exposed to in an aquaculture pond the degree of biocontrol provided by Bacillus strains would be of an even greater magnitude.

The challenge study with striped catfish revealed reduced levels of mortality due to E. ictaluri for all of Bacillus strains, especially with the use of strain AP79 that reduced mortality to only 9.7% compared to the control level of 70.8% mortality. It is interesting that the relative biocontrol activity of tested Bacillus strains was different in the two catfish species. This could reflect a biologically meaningful difference in the interactions between Bacillus strains and their respective host. Also, there could be unique tripartite interactions between host, pathogen, and probiotic bacteria that could be influenced by environmental factors. Clearly more research is needed to understand the complex interplay between host, pathogen and probiotic Bacillus strains, and how to manipulate the environment to achieve the optimal biological control of disease. Further studies using an aquarium disease model with static conditions need to be conducted to optimize important parameters for challenge such as dosage and timing with the best performing Bacillus strains, with subsequent studies at a pond-scale to evaluate biological control efficacy within an aquaculture pond ecosystem.

One of the safety requirements for live bacteria directly consumed by humans is the absence of any acquired resistance to clinically important antibiotics (Sorokulova 2008). Although the Bacillus strains used in this research were not for direct consumption by humans, they might be consumed inadvertently, as their hosts were cultured for food. Thus, it is important to analyze antibiotic resistance in probiotic strains and to distinguish the natural resistance, which is one of the phenotypic characteristics of a species, and acquired (i.e., transferable) resistance, which is associated with occurrence of plasmids. Also, pathogenicity and enterotoxin production are closely associated with plasmids (Pannucci et al. 2002). None of the selected Bacillus strains carried any plasmids, and each of the strains was susceptible to a broad spectrum of antibiotics tested, which ensures their inability to conjugally transfer any plasmid that might confer antibiotic resistance.

Knowledge of the secondary metabolites expressed by each Bacillus strain may improve the rational selection of strains and strain “cocktails” to enhance biological control efficacy against aquaculture pathogens. Bacillus strains with similar antibiosis profiles against aquaculture and plant pathogens may be grouped together (Kloepper et al. 2004). The antimicrobial compound(s) produced by strains from different antibiosis groups should be different. Presumably the combination of strains from different antibiosis groups will provide even greater biocontrol of disease due to production of multiple antibiotic compounds acting by different mechanisms. Diffusible antimicrobial compounds were clearly involved in the in vitro antagonistic activity observed in soft agar overlay and in diffusion tests. The relative importance of secondary metabolites for in vivo biological control is unknown compared to enhancing fish immune competence and/or competitive exclusion mechanisms of pathogen antagonism. Future studies will investigate the relative contribution of specific antibiotic compounds to the biological control activity of some Bacillus strains.

In conclusion, a collection of Bacillus strains was identified that are antagonistic to the primary pathogens of catfish and are beneficial to both channel catfish and striped catfish when administered on feed for the control of ESC and BNP, respectively. These bacteria have potential application in aquaculture as a cost-effective alternative to the current use of antimicrobial compounds.

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It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention. Thus, it should be understood that although the present invention has been illustrated by specific embodiments and optional features, modification and/or variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

Citations to a number of patent and non-patent references are made herein. The cited references are incorporated by reference herein in their entireties. In the event that there is an inconsistency between a definition of a term in the specification as compared to a definition of the term in a cited reference, the term should be interpreted based on the definition in the specification.

TABLE 1 Antimicrobial activity of 22 Bacillus strains against pathogens. Aeromonas Edwardsiella Edwardsiella Flavobacterium Saprolegnia Streptococcus Yersinia Phylogeny Strain hydrophila ictaluri tarda columnare ferax iniae ruckeri B. subtilis group AB01 + + + +++ + ++ ++ B. pumilus ^(‡) AP18 + + − − + + − B. subtilis group AP71 + ++ + − − ++ + B. cereus AP76 + ++ ++ − + ++ ++ B. subtilis group AP77 + +++ ++ − + + ++ B. subtilis group, AP79 ++ ++ + − − ++ ++ B. amyloliquefaciens^(‡) B. subtilis group AP102 + ++ ++ ++ + − ++ B. subtilis group, AP143 ++ ++ ++ − + + ++ B. amyloliquefaciens ^(‡) B. subtilis group AP183 + ++ ++ − − ++ + B. subtilis group AP189 ++ +++ ++ − − ++ + B. methylotrophicus AP191 ++ +++ + + + ++ − B. subtilis group, AP193L ++ ++ ++ ++ + + − B. amyloliquefaciens ^(‡) B. subtilis group AP215 + +++ + − + + ++ B. subtilis group AP218 + ++ + − + + + B. subtilis group AP219 ++ ++ + + + ++ + B. subtilis group, AP254L + ++ + ++ − − − B. amyloliquefaciens ^(‡) B. pumilus AP280 + ++ + − + + + B. subtilis group AP295 + ++ + − + + ++ B. subtilis group AP301 + ++ + +++ + ++ + B. subtilis group AP303 ++ ++ ++ − + + ++ B. subtilis group AP305 ++ ++ ++ − − + ++ (+) Zone of inhibition up to 5 mm; (++) Zone of inhibition from 5 mm to 1 cm; (+++) Zone of inhibition greater than 1 cm. (−) No observable zone of inhibition. ^(‡)Phylogenetic affiliation inferred from a comparison of these Bacillus strain genome sequences with previously sequenced Bacillus genomes.

TABLE 2 Mortality (%) (±SE) of groups of fish that received feed amended with different Bacillus strains or control feed and were challenged with E. ictaluri (n = 4). Channel catfish Channel catfish Striped catfish challenge challenge challenge Treatment (FIG. 5.A) (FIG. 5.B) (FIG. 5.C) Control 98.0 ± 1.16^(a ) 41.3 ± 5.91^(a) 70.8 ± 7.31^(a )  AB01 84.8 ± 1.95^(bc) 37.5 ± 9.46^(a) 56.9 ± 6.56^(ab)  AP143 83.1 ± 2.88^(bc)  43.3 ± 14.81^(a) Not determined AP193L 95.0 ± 3.00^(ab) 35.0 ± 5.40^(a) 30.6 ± 23.73^(ab) AP254L 93.7 ± 2.79^(ab) Not determined 54.2 ± 11.43^(ab) AP79  89.0 ± 2.74^(abc) 46.3 ± 5.15^(a) 9.7 ± 6.56^(b)  Means in the same column sharing a common superscript letter were not significantly different (P > 0.05) as determined by Tukey's test. 

The invention claimed is:
 1. A pelleted feed composition for aquatic animals, wherein the feed is provided with a coating and the feed composition comprises a spore-forming strain of Bacillus having a 16S rDNA sequence comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3, or comprising a 16S rDNA sequence having at least 99% sequence identity to SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3, wherein the spore-forming strain of the Bacillus is present at a concentration of at least 10⁴ CFU/g of the feed composition.
 2. The feed composition of claim 1, wherein the spore-forming strain of the Bacillus is a Bacillus species having a 16S rDNA comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO:
 3. 3. The feed composition of claim 1, wherein the spore-forming strain of the Bacillus is susceptible to one or more antibiotics selected from the group consisting of carbenicillin, ampicillin, spectinomycin, oxacillin, vancomycin, cephalothin, novobiocin, sulfadiazine, amikacin, erythromycin, neomycin, penicillin, chloramphenicol, sulfamethoxazole, norfloxacin, gentamicin and ciprofloxacin.
 4. The feed composition of claim 1, wherein the feed composition is a feed composition for farmed fish.
 5. The feed composition of claim 1, wherein the spore-forming strain of the Bacillus is the single strain of Bacillus present in the feed composition.
 6. The feed composition of claim 1, wherein the composition comprises a mixture of spore-forming strains of Bacillus.
 7. The feed composition of claim 1, wherein the spore-forming strain of the Bacillus is selected from the group consisting of Bacillus strains deposited under the accession numbers NRRL B-50745, NRRL B-50741, NRRL B-50742, NRRL B-50743, and NRRL B-50744.
 8. A pelleted feed composition for aquatic animals, wherein the feed is provided with a coating and the feed composition comprises a spore-forming strain of Bacillus, wherein the spore-forming strain of Bacillus is a Bacillus species having a 16S rDNA comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3, and the spore-forming strain of the Bacillus is present at a concentration of at least 10⁴ CFU/g of the feed composition.
 9. The feed composition of claim 8, wherein the spore-forming strain of the Bacillus inhibits the growth of one or more bacteria selected from the group consisting of Aeromonas hydrophila, Flavobacterium columnare, Edwardsiella ictaluri, Edwardsiella tarda, Streptococcus iniae, and Yersinia ruckeri.
 10. A pelleted feed composition for aquatic animals, wherein the feed is provided with a coating and the feed composition comprises a spore-forming strain of Bacillus selected from the group consisting of Bacillus strains deposited under the accession numbers NRRL B-50745, NRRL B-50741, NRRL B-50742, NRRL B-50743, and NRRL B-50744, and wherein the spore-forming strain of the Bacillus is present at a concentration of at least 10⁴ CFU/g of the feed composition. 